What are some ways of training in the dojo that would help better prepare a person for a physical confrontation with another person? I understand there are all kinds of variables but lets just look at the basic, two people getting into a fight. I also understand that Aikido is much more than just the physical techniques and there are many other great benefits for practicing aikido. That is why I have trained in aikido as long as I have.

To my mind the "whys" which lead to a physical confrontation are good for prevention, but for dealing with one it's best to look at the underlying principles of force and timing and then tweak them by applying different constraints.
For dealing with resistance levels, I like the method of graduating the intensity: starting out with no resistance and then applying very little, then a bit more and so on. How far to go with it depends on the abilities of the parties involved, but that's one good way to see how resistance levels affect waza.
I also really like kaeshiwaza because it teaches possibilities for regaining the initiative and shows some important factors for how that can be done in the first place. I feel like I've learned a lot about proper posture and engagement/relaxation from kaeshi waza...relatively speaking anyway.
One of the most important aspects of training for me has to do with dealing with different body types because they have different structural qualities. Different people generate power from different parts of the body, sometimes dramatically so. So with that in mind I guess I'd suggest trying to think of variables like that and then playing with them individually. For example, trying the same technique at different ranges (arms almost fully extended; almost fully "contracted;" one arm constrained; etc.).
Graduated speed is another training method I personally like. Training slow I like that it allows me to explore the moment a bit more, while training somewhat fast I have to learn how to move without thinking.
...Stuff like that.
Gambatte!
Matt